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Announcing CytoSEED plugin for viewing metabolic models from the Model SEED
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Matt DeJongh  
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 More options Oct 31 2011, 8:24 pm
From: Matt DeJongh <mkdejo...@gmail.com>
Date: Mon, 31 Oct 2011 17:24:56 -0700 (PDT)
Local: Mon, Oct 31 2011 8:24 pm
Subject: Announcing CytoSEED plugin for viewing metabolic models from the Model SEED
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The Hope College bioinformatics team is pleased to announce the
release of version 1.1 of the CytoSEED viewer for metabolic models
generated by the Model SEED (http://www.theseed.org/models).

CytoSEED is a plugin for Cytoscape 2.8, and enables viewing,
manipulating and analyzing metabolic models created using the Model
SEED.  Users may load any public or private model for which they have
access in the Model SEED. CytoSEED downloads the model data, reactions
and compounds
from the Model SEED, and organizes the reactions into networks based
on their corresponding KEGG pathway maps. After the initial load
(which may take several minutes), the model data is stored on the
user's desktop in a specified folder for quick loading in subsequent
sessions.

CytoSEED can be downloaded from the Cytoscape Plugin Manager, and also
from
http://sourceforge.net/projects/cytoseed/files/ along with a Tutorial
and a Quick Installation guide.

CytoSEED's capabilities include:
* Downloading models from the Model SEED; creation of Cytoscape
sessions for viewing models; saving and reopening Cytoscape sessions
* Creation and deletion of pathway maps; moving/copying reactions
between pathway maps; hiding/showing nodes within pathway maps
* Saving pathway map formatting so that it can be loaded and applied
to other models
* Visualization of Flux Variability Analysis results in multiple
media; reactions are colored based on
essential/active/inactive/gap-filled categories
* Capability to open models for multiple organisms in one Cytoscape
session, to enable comparative model analysis
* Visualization of Flux Balance Analysis results
* Gene Expression Analysis results (in development)

Please send your questions and comments to dejo...@hope.edu


 
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